[Objective] Jilong Valley will be an important area for major engineering projects across the Himalayas in Tibet in the future for a long time. However, we still lack a systematic understanding of the basic geological characteristics, especially the N-S-trending structure, which may induce unexpected engineering construction risks. [Methods] Field geological survey, joint statistics, geothermal investigation, audio frequency magnetotelluric sounding and calcite U-series dating were conducted to reveal the characteristics of the N-S-trending faults and joints in Jilong Valley, and through this to explore the main engineering geological risks related to the N-S-trending structures. [Results] The N-S-trending faults in Jilong Valley are generally small in scale, partially cutting through the high Himalayan belt, and also the basin controlling faults of Jilong Basin. The formation and sedimentary evolution of Jilong Basin were controlled by the four N-S-trending normal faluts in its east boundary and interior. The seismic rocks near the east boundary faults and syn-sedimentary faults in the basin indicate that the Jilong basin has intermittent activity characteristics. The regional permeable distribution is displayed by the N-S-trending joints, which were formed in a simialr stress field controlled by the N-S-trending rift. [Conclusions] The N-S-trending structure in Jilong Valley are potential engineering geological risk sources, according to its Holocene activity and its control over regional geothermal, and collapse, landslide, debris flow geological disasters. We propose that the North-South structure will be one of the important directions of geological safety risk assessment for the planning and construction of Jilong Valley major engineering project.